I am trying to do visualizations of the charge density for non-spin-polarized silicon nanowire. After relaxation, I try to run grid2cube with the following syntax (my input file for g2c is SiNW.g2c and for simplicity's sake, my system label will be referred to as S_L):
./grid2cube.out < SiNW.g2c S_L.XV S_L.RHO > g2c.out
but when I do this, it returns that my nspin=0 and thus does not make a
.cube file at all.
My input file for g2c is:
---------
S_L
rho
0.0 0.0 0.0
1
unformatted
----------
This is the standard output of the command that I issued above:
------
Cell vectors
46.1754762584164 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 46.1754762584164 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 17.7734538727118
Grid mesh: 216 x 0 x 216
nspin = 0
-------
Something seems strange to me about that '0' in the grid mesh, too.
I tried editing the fortran code for grid2cube.f, setting nspin=1 manually
inside the code, recompiling and running again, but this is what I get:
---------
68 0.000000 0.000000 0.000000
216 0.213775 0.000000 0.000000
0 NaN Infinity NaN
216 0.000000 0.000000 0.082285
14 0.000000 9.433099 NaN 0.903102
14 0.000000 9.432789 NaN 5.318021
14 0.000000 13.033586 NaN 6.808950
14 0.000000 13.015757 NaN 11.235454
14 0.000000 13.015924 NaN 12.758808
14 0.000000 13.034385 NaN 17.185759
14 0.000000 16.618908 NaN 0.904276
14 0.000000 16.618154 NaN 5.315916
14 0.000000 13.005918 NaN 0.916227
14 0.000000 13.038506 NaN 5.327205
14 0.000000 16.613020 NaN 6.851160
14 0.000000 16.601408 NaN 11.252581
14 0.000000 5.860178 NaN 0.916193
14 0.000000 5.827284 NaN 5.327166
14 0.000000 9.433099 NaN 6.820480
14 0.000000 9.432860 NaN 11.246750
14 0.000000 9.432089 NaN 12.764217
14 0.000000 9.432765 NaN 17.163633
14 0.000000 2.246604 NaN 0.904218
14 0.000000 2.245486 NaN 5.316090
14 0.000000 5.830740 NaN 6.808691
14 0.000000 5.849300 NaN 11.235654
14 0.000000 5.848824 NaN 12.758320
14 0.000000 5.831752 NaN 17.185301
14 0.000000 5.828020 NaN 0.893063
14 0.000000 5.859017 NaN 5.304081
14 0.000000 9.431658 NaN 6.829797
14 0.000000 9.431909 NaN 11.229134
----------
And this is obviously a non-result.
Additionally, I read on the boards something about using a program called
WSxM for visualization of SIESTA output. I downloaded the program, but could
not get it to load any of my output files for plotting. Anybody use this
regularly for plotting SIESTA output?
I also could not find the keywords to save RHO, DRHO, etc. in formatted
output. I think that may have something to do with this, at least maybe for
the WSxM part. My fdf file is attached for any who wish to help me tackle my
problem. Any suggestions would be appreciated, and I understand that in the
past few days there has been a lot of activity in the email list.
Thank you in advance for your kind help,
Abraham Hmiel
Research Assistant in Theoretical and Computational Nanoscience
Center for Nanoscale Science and Engineering at the State University of New
York at Albany
SiNW.fdf
Description: application/vnd.fdf
